She was undoing what the Great Intelligence was doing. That line about twisting the Doctor’s Timelines. I’m under the impression that basically splintered into a million pieces, and she used a nearby tool in each one to knock out the Great Intelligence, or in a few cases, intervened directly. Like with the TARDIS. In that case, she served as a matchmaker of sorts, being a reference for the TARDIS we know and love. The Doctor went into the other one, became attached to it and “voila.”

Truthfully, I don’t mind this development. Remember, Rose became a human incarnation of the Time Vortex, and obliterated a huge number of Daleks. Clara essentially Bad-Wolfed. And River, which I feel better about now, has also met all the Doctors. Hell, some of the other canon stuff is even weirder.[/spoilers]

At some point now, I think there should be discussions between J.K. Rowling and the Doctor Who crew on her writing an episode or something.